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- PDB-4b8t: RNA BINDING PROTEIN Solution structure of the third KH domain of ... -

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Basic information

Entry
Database: PDB / ID: 4b8t
TitleRNA BINDING PROTEIN Solution structure of the third KH domain of KSRP in complex with the G-rich target sequence.
Components
  • 5'-R(*AP*GP*GP*GP*UP)-3'
  • KH-TYPE SPLICING REGULATORY PROTEIN
KeywordsTRANSCRIPTION/RNA / TRANSCRIPTION-RNA COMPLEX
Function / homology
Function and homology information


positive regulation of mRNA catabolic process / ATF4 activates genes in response to endoplasmic reticulum stress / 3'-UTR-mediated mRNA destabilization / miRNA metabolic process / negative regulation of nitric oxide biosynthetic process / mRNA 3'-UTR AU-rich region binding / RNA splicing, via transesterification reactions / negative regulation of low-density lipoprotein particle clearance / KSRP (KHSRP) binds and destabilizes mRNA / cellular response to cytokine stimulus ...positive regulation of mRNA catabolic process / ATF4 activates genes in response to endoplasmic reticulum stress / 3'-UTR-mediated mRNA destabilization / miRNA metabolic process / negative regulation of nitric oxide biosynthetic process / mRNA 3'-UTR AU-rich region binding / RNA splicing, via transesterification reactions / negative regulation of low-density lipoprotein particle clearance / KSRP (KHSRP) binds and destabilizes mRNA / cellular response to cytokine stimulus / mRNA transport / regulation of mRNA stability / protein folding chaperone / RNA splicing / mRNA processing / mRNA binding / regulation of transcription by RNA polymerase II / DNA binding / RNA binding / nucleoplasm / nucleus / membrane / cytoplasm / cytosol
Similarity search - Function
: / : / : / : / Far upstream element-binding protein, C-terminal / Far upstream element-binding protein, C-terminal / K Homology domain, type 1 / KH domain / K Homology domain, type 1 / Ribosomal Protein S8; Chain: A, domain 1 ...: / : / : / : / Far upstream element-binding protein, C-terminal / Far upstream element-binding protein, C-terminal / K Homology domain, type 1 / KH domain / K Homology domain, type 1 / Ribosomal Protein S8; Chain: A, domain 1 / Type-1 KH domain profile. / K Homology domain, type 1 superfamily / K Homology domain / K homology RNA-binding domain / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
RNA / Far upstream element-binding protein 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
SYNTHETIC CONSTRUCT (others)
MethodSOLUTION NMR / ARIA
AuthorsNicastro, G. / Garcia-Mayoral, M.F. / Hollingworth, D. / Kelly, G. / Martin, S.R. / Briata, P. / Gherzi, R. / Ramos, A.
Citation
Journal: Nat.Struct.Mol.Biol. / Year: 2012
Title: Noncanonical G Recognition Mediates Ksrp Regulation of Let-7 Biogenesis
Authors: Nicastro, G. / Garcia-Mayoral, M.F. / Hollingworth, D. / Kelly, G. / Martin, S.R. / Briata, P. / Gherzi, R. / Ramos, A.
#1: Journal: Structure / Year: 2007
Title: The Structure of the C-Terminal Kh Domains of Ksrp Reveals a Noncanonical Motif Important for Mrna Degradation.
Authors: Garcia-Mayoral, M.F. / Hollingworth, D. / Masino, L. / Diaz-Moreno, I. / Kelly, G. / Gherzi, R. / Chou, C. / Chen, C. / Ramos, A.
History
DepositionAug 30, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 7, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 21, 2012Group: Database references
Revision 1.2Nov 28, 2012Group: Other / Structure summary
Revision 1.3Dec 5, 2012Group: Atomic model
Revision 1.4Jan 16, 2013Group: Database references
Revision 1.5May 15, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_cs / _pdbx_database_status.status_code_mr / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: KH-TYPE SPLICING REGULATORY PROTEIN
B: 5'-R(*AP*GP*GP*GP*UP)-3'


Theoretical massNumber of molelcules
Total (without water)12,5392
Polymers12,5392
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1

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Components

#1: Protein KH-TYPE SPLICING REGULATORY PROTEIN


Mass: 10912.468 Da / Num. of mol.: 1 / Fragment: THIRD KH DOMAIN, RESIDUES 317-418
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q92945
#2: RNA chain 5'-R(*AP*GP*GP*GP*UP)-3'


Mass: 1626.032 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR detailsText: NONE

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Sample preparation

DetailsContents: 10% WATER/90% D2O
Sample conditionsIonic strength: 100 MM NACL / pH: 7.4 / Pressure: 1.0 atm / Temperature: 298.0 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 700 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CNSBRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU,READ, RICE,SIMONSON,WARRENrefinement
UXNMR3.5structure solution
VNMRstructure solution
NMRPipestructure solution
Sparkystructure solution
ARIA1.2structure solution
RefinementMethod: ARIA / Software ordinal: 1
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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